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- PDB-4aq0: Structure of the Gh92 Family Glycosyl Hydrolase Ccman5 in complex... -

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Basic information

Entry
Database: PDB / ID: 4aq0
TitleStructure of the Gh92 Family Glycosyl Hydrolase Ccman5 in complex with deoxymannojirimycin
ComponentsCCMAN5
KeywordsHYDROLASE / MANNOSIDASE
Function / homology
Function and homology information


alpha-mannosidase / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / glycoprotein catabolic process / alpha-mannosidase activity / carbohydrate binding / carbohydrate metabolic process / metal ion binding / cytosol
Similarity search - Function
Glycosyl hydrolase family 92 / Glycosyl hydrolase family 92 N-terminal domain / Glycosyl hydrolase family 92 catalytic domain / Glycosyl hydrolase family 92 N-terminal domain / : / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Six-hairpin glycosidase superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
1-DEOXYMANNOJIRIMYCIN / Ccman5
Similarity search - Component
Biological speciesCELLULOSIMICROBIUM CELLULANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsBaranova, E. / Tiels, P. / Callewaert, N. / Remaut, H.
CitationJournal: Nat.Biotechnol. / Year: 2012
Title: A Bacterial Glycosidase Enables Mannose-6-Phosphate Modification and Improved Cellular Uptake of Yeast-Produced Recombinant Human Lysosomal Enzymes.
Authors: Tiels, P. / Baranova, E. / Piens, K. / De Visscher, C. / Pynaert, G. / Nerinckx, W. / Stout, J. / Fudalej, F. / Hulpiau, P. / Tannler, S. / Geysens, S. / Van Hecke, A. / Valevska, A. / ...Authors: Tiels, P. / Baranova, E. / Piens, K. / De Visscher, C. / Pynaert, G. / Nerinckx, W. / Stout, J. / Fudalej, F. / Hulpiau, P. / Tannler, S. / Geysens, S. / Van Hecke, A. / Valevska, A. / Vervecken, W. / Remaut, H. / Callewaert, N.
History
DepositionApr 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CCMAN5
B: CCMAN5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,1116
Polymers168,5862
Non-polymers5264
Water18,7721042
1
A: CCMAN5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6153
Polymers84,2931
Non-polymers3222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CCMAN5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4963
Polymers84,2931
Non-polymers2032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.620, 91.790, 224.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein CCMAN5


Mass: 84292.852 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-774
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL FRAGMENT CORRESPONDING TO CATALYTIC DOMAIN.
Source: (gene. exp.) CELLULOSIMICROBIUM CELLULANS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: M1E1E9*PLUS, alpha-mannosidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Chemical ChemComp-DMJ / 1-DEOXYMANNOJIRIMYCIN


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1042 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.69 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2 M NA FLUORIDE, 0.1 M BIS TRIS PROPANE PH 7.5 AND 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.0725
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0725 Å / Relative weight: 1
ReflectionResolution: 2.1→55.5 Å / Num. obs: 95933 / % possible obs: 100 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.9
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XSG

2xsg


Resolution: 2.09→55.5 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.764 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20349 5040 5 %RANDOM
Rwork0.17027 ---
obs0.17194 95933 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.283 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2---0.08 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.09→55.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11513 0 24 1042 12579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02111822
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0961.93616138
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.64551527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59923.891550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.663151632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.491572
X-RAY DIFFRACTIONr_chiral_restr0.0740.21750
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219368
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3711.57541
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.724212017
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.32334281
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1764.54121
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.086→2.14 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 364 -
Rwork0.239 6991 -
obs--100 %

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